2QEX image
Deposition Date 2007-06-26
Release Date 2008-09-30
Last Version Date 2023-08-30
Entry Detail
PDB ID:
2QEX
Keywords:
RIBOSOME
Title:
Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit
Biological Source:
Source Organism:
Haloarcula marismortui (Taxon ID: 2238)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.90 Å
R-Value Free:
0.24
R-Value Work:
0.20
Space Group:
C 2 2 21
2QEX validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: 0)
Chain Length:2772
Number of Molecules:1
Biological Source:Haloarcula marismortui
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37e
Gene (Uniprot):rpl37e
Chain IDs:BA (auth: 1)
Chain Length:57
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32410 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L39e
Gene (Uniprot):rpl39e
Chain IDs:CA (auth: 2)
Chain Length:50
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22452 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L44e
Gene (Uniprot):rpl44e
Chain IDs:DA (auth: 3)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32411 Pfam ID:PF00935
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2P
Gene (Uniprot):rpl2
Chain IDs:C (auth: A)
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20276 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3P
Gene (Uniprot):rpl3
Chain IDs:D (auth: B)
Chain Length:338
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20279 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4P
Gene (Uniprot):rpl4
Chain IDs:E (auth: C)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12735 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5P
Gene (Uniprot):rpl5
Chain IDs:F (auth: D)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14124 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6P
Gene (Uniprot):rpl6
Chain IDs:G (auth: E)
Chain Length:178
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14135 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7Ae
Gene (Uniprot):rpl7ae
Chain IDs:H (auth: F)
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12743 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acidic ribosomal protein P0 homolog
Gene (Uniprot):rpl10
Chain IDs:I (auth: G)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P15825 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10e
Gene (Uniprot):rpl10e
Chain IDs:J (auth: H)
Chain Length:174
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60617 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11P
Gene (Uniprot):rpl11
Chain IDs:EA (auth: I)
Chain Length:162
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14122 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13P
Gene (Uniprot):rpl13
Chain IDs:K (auth: J)
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P29198 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14P
Gene (Uniprot):rpl14
Chain IDs:L (auth: K)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22450 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15P
Gene (Uniprot):rpl15
Chain IDs:M (auth: L)
Chain Length:165
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12737 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15e
Gene (Uniprot):rpl15e
Chain IDs:N (auth: M)
Chain Length:196
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60618 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18P
Gene (Uniprot):rpl18
Chain IDs:O (auth: N)
Chain Length:187
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14123 Pfam ID:PF17144
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18e
Gene (Uniprot):rpl18e
Chain IDs:P (auth: O)
Chain Length:116
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12733 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19e
Gene (Uniprot):rpl19e
Chain IDs:Q (auth: P)
Chain Length:149
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14119 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21e
Gene (Uniprot):rpl21e
Chain IDs:R (auth: Q)
Chain Length:96
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12734 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22P
Gene (Uniprot):rpl22
Chain IDs:S (auth: R)
Chain Length:155
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10970 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23P
Gene (Uniprot):rpl23
Chain IDs:T (auth: S)
Chain Length:85
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12732 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24P
Gene (Uniprot):rpl24
Chain IDs:U (auth: T)
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10972 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24e
Gene (Uniprot):rpl24e
Chain IDs:V (auth: U)
Chain Length:67
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14116 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29P
Gene (Uniprot):rpl29
Chain IDs:W (auth: V)
Chain Length:71
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10971 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30P
Gene (Uniprot):rpl30
Chain IDs:X (auth: W)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14121 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31e
Gene (Uniprot):rpl31e
Chain IDs:Y (auth: X)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P18138 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32e
Gene (Uniprot):rpl32e
Chain IDs:Z (auth: Y)
Chain Length:241
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12736 Pfam ID:PF14520, PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37Ae
Gene (Uniprot):rpl37ae
Chain IDs:AA (auth: Z)
Chain Length:73
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60619 Pfam ID:PF01780
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA A A ?
OMG A G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
OMU A U O2'-METHYLURIDINE 5'-MONOPHOSPHATE
PSU A U PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3 A U 3-METHYLURIDINE-5'-MONOPHOSHATE
Ligand Molecules
CD
CL
K
MG
NA
NEG
Primary Citation
Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.
Antimicrob.Agents Chemother. 51 4462 4465 (2007)
PMID: 17664317 DOI: 10.1128/AAC.00455-07

Abstact

Negamycin, a small-molecule inhibitor of protein synthesis, binds the Haloarcula marismortui 50S ribosomal subunit at a single site formed by highly conserved RNA nucleotides near the cytosolic end of the nascent chain exit tunnel. The mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.

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Protein

Chemical

Disease

Primary Citation of related structures
2QEX